private void AddDigestionTask_Click(object sender, RoutedEventArgs e)
{
// disable button so that no more tasks are added
AddDigestionTask.IsEnabled = false;
ResetDigestionTask.IsEnabled = true;
// disable fields to show that those parameters are used for the task
ProteaseSelectedForUse.IsEnabled = false;
MissedCleavagesTextBox.IsEnabled = false;
MinPeptideLengthTextBox.IsEnabled = false;
MaxPeptideLengthTextBox.IsEnabled = false;
DigestionTask task = new DigestionTask();
UpdateFieldsFromUser(task);
AddTaskToCollection(task);
OutputFolderTextBox.IsEnabled = true;
// output folder
if (string.IsNullOrWhiteSpace(OutputFolderTextBox.Text))
{
var pathOfFirstSpectraFile = System.IO.Path.GetDirectoryName(ProteinDbObservableCollection.First().FilePath);
OutputFolderTextBox.Text = System.IO.Path.Combine(pathOfFirstSpectraFile, @"$DATETIME");
}
var startTimeForAllFilenames = DateTime.Now.ToString("yyyy-MM-dd-HH-mm-ss", CultureInfo.InvariantCulture);
string outputFolder = OutputFolderTextBox.Text.Replace("$DATETIME", startTimeForAllFilenames);
OutputFolderTextBox.Text = outputFolder;
UserParameters.OutputFolder = outputFolder;
}
private void AddDigestionTask_Click(object sender, RoutedEventArgs e)
{
DigestionTask task = new DigestionTask();
UpdateFieldsFromUser(task);
AddTaskToCollection(task);
}
private void UpdateFieldsFromUser(DigestionTask run)
{
run.DigestionParameters.NumberOfMissedCleavagesAllowed = Convert.ToInt32(MissedCleavagesTextBox.Text);
run.DigestionParameters.MinPeptideLengthAllowed = Convert.ToInt32(MinPeptideLengthTextBox.Text);
run.DigestionParameters.MaxPeptideLengthAllowed = Convert.ToInt32(MaxPeptideLengthTextBox.Text);
run.DigestionParameters.TreatModifiedPeptidesAsDifferent = Convert.ToBoolean(ModPepsAreUnique.IsChecked);
List <Protease> proteases = new List <Protease>();
foreach (var protease in ProteaseSelectedForUse.SelectedItems)
{
proteases.Add(ProteaseDictionary.Dictionary[protease.ToString()]);
}
run.DigestionParameters.ProteasesForDigestion = proteases;
}
public static void SingleDatabase()
{
Loaders.LoadElements();
string subFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DigestionTest");
Directory.CreateDirectory(subFolder);
string databasePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "Databases", "TestDatabase_1.fasta");
DbForDigestion database = new DbForDigestion(databasePath);
Parameters param = new Parameters();
param.MinPeptideLengthAllowed = 1;
param.MaxPeptideLengthAllowed = 100;
param.NumberOfMissedCleavagesAllowed = 0;
param.TreatModifiedPeptidesAsDifferent = false;
param.ProteasesForDigestion.Add(ProteaseDictionary.Dictionary["trypsin"]);
param.OutputFolder = subFolder;
DigestionTask digestion = new DigestionTask();
digestion.DigestionParameters = param;
var digestionResults = digestion.RunSpecific(subFolder, new List <DbForDigestion>()
{
database
});
Assert.AreEqual(1, digestionResults.PeptideByFile.Count);
Assert.AreEqual(1, digestionResults.PeptideByFile.Values.Count);
Assert.AreEqual(2, digestionResults.PeptideByFile[database.FileName][param.ProteasesForDigestion.First().Name].Count);
foreach (var entry in digestionResults.PeptideByFile[database.FileName][param.ProteasesForDigestion.First().Name])
{
if (entry.Key.Accession == "testProtein_1")
{
Assert.AreEqual(26, entry.Value.Count);
Assert.AreEqual("MSFVNGNEIFTAAR", entry.Value[0].BaseSequence);
Assert.IsFalse(entry.Value[0].Unique);
Assert.IsFalse(entry.Value[0].UniqueAllDbs);
Assert.IsTrue(entry.Value[0].SeqOnlyInThisDb);
Assert.AreEqual("QGHYAVGAFNTNNLEWTR", entry.Value[1].BaseSequence);
Assert.IsTrue(entry.Value[1].Unique);
Assert.IsTrue(entry.Value[1].UniqueAllDbs);
Assert.IsTrue(entry.Value[1].SeqOnlyInThisDb);
Assert.AreEqual("AILK", entry.Value[2].BaseSequence);
Assert.IsTrue(entry.Value[2].Unique);
Assert.IsTrue(entry.Value[2].UniqueAllDbs);
Assert.IsTrue(entry.Value[2].SeqOnlyInThisDb);
Assert.AreEqual("AAQEK", entry.Value[3].BaseSequence);
Assert.IsFalse(entry.Value[3].Unique);
Assert.IsFalse(entry.Value[3].UniqueAllDbs);
Assert.IsTrue(entry.Value[3].SeqOnlyInThisDb);
Assert.AreEqual("NTPVLIQVSMGAAK", entry.Value[4].BaseSequence);
Assert.IsFalse(entry.Value[4].Unique);
Assert.IsFalse(entry.Value[4].UniqueAllDbs);
Assert.IsTrue(entry.Value[4].SeqOnlyInThisDb);
Assert.AreEqual("YMGDYK", entry.Value[5].BaseSequence);
Assert.IsFalse(entry.Value[5].Unique);
Assert.IsFalse(entry.Value[5].UniqueAllDbs);
Assert.IsTrue(entry.Value[5].SeqOnlyInThisDb);
Assert.AreEqual("LVK", entry.Value[6].BaseSequence);
Assert.IsFalse(entry.Value[6].Unique);
Assert.IsFalse(entry.Value[6].UniqueAllDbs);
Assert.IsTrue(entry.Value[6].SeqOnlyInThisDb);
Assert.AreEqual("TLVEEEMR", entry.Value[7].BaseSequence);
Assert.IsTrue(entry.Value[7].Unique);
Assert.IsTrue(entry.Value[7].UniqueAllDbs);
Assert.IsTrue(entry.Value[7].SeqOnlyInThisDb);
}
else if (entry.Key.Accession == "testProtein_2")
{
Assert.AreEqual(27, entry.Value.Count);
Assert.AreEqual("MSFVNGNEIFTAAR", entry.Value[0].BaseSequence);
Assert.IsFalse(entry.Value[0].Unique);
Assert.IsFalse(entry.Value[0].UniqueAllDbs);
Assert.IsTrue(entry.Value[0].SeqOnlyInThisDb);
Assert.AreEqual("QGHPPGAFNTNNLEWTR", entry.Value[1].BaseSequence);
Assert.IsTrue(entry.Value[1].Unique);
Assert.IsTrue(entry.Value[1].UniqueAllDbs);
Assert.IsTrue(entry.Value[1].SeqOnlyInThisDb);
Assert.AreEqual("AIVK", entry.Value[2].BaseSequence);
Assert.IsTrue(entry.Value[2].Unique);
Assert.IsTrue(entry.Value[2].UniqueAllDbs);
Assert.IsTrue(entry.Value[2].SeqOnlyInThisDb);
Assert.AreEqual("AAQEK", entry.Value[3].BaseSequence);
Assert.IsFalse(entry.Value[3].Unique);
Assert.IsFalse(entry.Value[3].UniqueAllDbs);
Assert.IsTrue(entry.Value[3].SeqOnlyInThisDb);
Assert.AreEqual("NTPVLIQVSMGAAK", entry.Value[4].BaseSequence);
Assert.IsFalse(entry.Value[4].Unique);
Assert.IsFalse(entry.Value[4].UniqueAllDbs);
Assert.IsTrue(entry.Value[4].SeqOnlyInThisDb);
Assert.AreEqual("YMGDYK", entry.Value[5].BaseSequence);
Assert.IsFalse(entry.Value[5].Unique);
Assert.IsFalse(entry.Value[5].UniqueAllDbs);
Assert.IsTrue(entry.Value[5].SeqOnlyInThisDb);
Assert.AreEqual("LVK", entry.Value[6].BaseSequence);
Assert.IsFalse(entry.Value[6].Unique);
Assert.IsFalse(entry.Value[6].UniqueAllDbs);
Assert.IsTrue(entry.Value[6].SeqOnlyInThisDb);
Assert.AreEqual("TLVEPPMR", entry.Value[7].BaseSequence);
Assert.IsTrue(entry.Value[7].Unique);
Assert.IsTrue(entry.Value[7].UniqueAllDbs);
Assert.IsTrue(entry.Value[7].SeqOnlyInThisDb);
}
}
Directory.Delete(subFolder, true);
}
